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The problem of dictionary matching is a classical problem in string matching: given a set S of d strings of total length n characters over an (not necessarily constant) alphabet of size sigma, build a data structure so that we can match in…
Network reconstruction consists in determining the unobserved pairwise couplings between $N$ nodes given only observational data on the resulting behavior that is conditioned on those couplings -- typically a time-series or independent…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
We revisit classic string problems considered in the area of parameterized complexity, and study them through the lens of dynamic data structures. That is, instead of asking for a static algorithm that solves the given instance efficiently,…
In the $k$-Edit Circular Pattern Matching ($k$-Edit CPM) problem, we are given a length-$n$ text $T$, a length-$m$ pattern $P$, and a positive integer threshold $k$, and we are to report all starting positions of the substrings of $T$ that…
Given a source of iid samples of edges of an input graph $G$ with $n$ vertices and $m$ edges, how many samples does one need to compute a constant factor approximation to the maximum matching size in $G$? Moreover, is it possible to obtain…
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…
In several combinatorial optimization problems arising in cryptography and design theory, the admissible solutions must often satisfy a balancedness constraint, such as being represented by bitstrings with a fixed number of ones. For this…
A family of comparison-based exact pattern matching algorithms is described. They utilize multi-dimensional arrays in order to process more than one adjacent text window in each iteration of the search cycle. This approach leads to a lower…
Although the applications of Non-Homogeneous Poisson Processes to model and study the threshold overshoots of interest in different time series of measurements have proven to provide good results, they needed to be complemented with an…
In the stochastic matching problem, we are given a general (not necessarily bipartite) graph $G(V,E)$, where each edge in $E$ is realized with some constant probability $p > 0$ and the goal is to compute a bounded-degree (bounded by a…
The maximum matching problem in dynamic graphs subject to edge updates (insertions and deletions) has received much attention over the last few years; a multitude of approximation/time tradeoffs were obtained, improving upon the folklore…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
We study optimization problems that are neither approximable in polynomial time (at least with a constant factor) nor fixed parameter tractable, under widely believed complexity assumptions. Specifically, we focus on Maximum Independent…
Given an indeterminate string pattern $p$ and an indeterminate string text $t$, the problem of order-preserving pattern matching with character uncertainties ($\mu$OPPM) is to find all substrings of $t$ that satisfy one of the possible…
In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the…
We resolve a long-standing open question, about the existence of a constant-factor approximation algorithm for the average-case \textsc{Decision Tree} problem with uniform probability distribution over the hypotheses. We answer the question…
The algorithmic tasks of computing the Hamming distance between a given pattern of length $m$ and each location in a text of length $n$ is one of the most fundamental algorithmic tasks in string algorithms. Unfortunately, there is evidence…
We study the problem of estimating the size of the maximum matching in the sublinear-time setting. This problem has been extensively studied, with several known upper and lower bounds. A notable result by Behnezhad (FOCS 2021) established a…
We study dynamic $(1-\epsilon)$-approximate rounding of fractional matchings -- a key ingredient in numerous breakthroughs in the dynamic graph algorithms literature. Our first contribution is a surprisingly simple deterministic rounding…